Murine splenocytes were radiolabeled with 3H- and 14C-amino acids; the Ia alloantigens encoded by the I-A and I-E/C subregions were isolated by immunoprecipitation and analyzed for structural variation by polyacrylamide gel electrophoresis. The I-A subregion products (k, d, and b haplotypes) are composed of two polypeptides, α and β, with m.w. of 34,000 and 26,000 daltons, respectively. Haplotype-associated differences in m.w. were detected in the I-E/C products of the k, r, p, and d haplotypes. The α and β chains of E/Ck and E/Cr are 34,000 and 28,000 daltons, respectively; E/Cp and E/Cd molecules are composed of 31,000 and 29,000 dalton polypeptides. Thus, there is both subregion (I-A vs I-E/C) and haplotype (E/Ck, E/Cr vs E/Cd, E/Cp) associated variation in the m.w. of the Ia alloantigens. Additionally, the covalent vs noncovalent association of the Ia subunits was examined and it was found that the α and β chains of both I-A and I-E/C are not covalently associated. However, the I-A α and β chains tend to associate through disulfide bonds during detergent lysis; the presence of alkylating agents during cell lysis prevents this association, and only free α and β chains are observed under nonreducing conditions.